6 replies to this topic

[ram]

I have a vector sequence and I want to search which universal primers can be used with this vector. Is there any online tool available for cheeking this?
Thanaks
Ram

[Adrian K]

what are you trying to do with the vector? are you try to sequence it?
usually T7 promoter or M13 is the common one... not sure if there is such a checking tool available.

[ram]

adrian kohsf, on 02 October 2010 - 04:05 AM, said:

what are you trying to do with the vector? are you try to sequence it?
usually T7 promoter or M13 is the common one... not sure if there is such a checking tool available.

No I already have a sequence, but I am not sure which universal primers can be used for checking the presence of this plasmid in cells and size of the insert. I was just searching for a program which after feeding the sequence will tell me which universal primer site dies the sequence has (although this can be searched manually)

[Adrian K]

I thought when you purchase your vector, there is mentioned somewhere in the brochure about the sequencing primers for that particular vector? Just PCR the both forward and reverse primers together will do? Or did I just misunderstood you?

[ram]

adrian kohsf, on 02 October 2010 - 09:45 AM, said:

I thought when you purchase your vector, there is mentioned somewhere in the brochure about the sequencing primers for that particular vector? Just PCR the both forward and reverse primers together will do? Or did I just misunderstood you?

Thanks for reply and sorry for incomplete information.
This is a old construct brought from somewhere else. I did not get much information about the universal primer regions in it. I just have the sequence. And I don't want to design new primers based on the sequence but I wish that out of the several universal primers that I have, few should have a complementary region in this construct!
The original question remains at the same place!     
"Is any online program available to find universal primer regions in a given sequence?"

[Adrian K]

you got the sequence, you got some primers, you can always try to search the binding site by using a word processor and your pair of good eyes.

Edited by adrian kohsf, 02 October 2010 - 11:33 PM.

[ram]

adrian kohsf, on 02 October 2010 - 11:05 PM, said:

you got the sequence, you got some primers, you can always try to search the binding site by using a word processor and your pair of good eyes.

Thanks for your reply.
Yah, definitely! As I wrote in one of my previous replies I can manually search the primer sequence in the construct. I had two intentions for asking the question: (1) to find out which universal primer regions does the construct have, irrespective of me having the primers (2) with the thought that if such program is available online, it might be helpful for me as well as for others reading Bioforum, I dropped the question which is still fundamentally unanswered.